Arghya Mukherjee
Research Ireland RD&I Fellow Fermented Foods, Probiotics, Gut Microbiome and Next-Generation SequencingResearch Interests
- Structure, function and physiology of microbiomes – understanding gut, food and environmental microbiomes through a combination of high throughput sequencing, bioinformatics, molecular biology and microbiological approaches
- Gut microbiome and health – gut microbiota and its association with suboptimal health conditions
- Probiotics and fermented foods – probiotics and functional fermented foods, particularly plant-based fermented foods, as therapeutic interventions
- Single-cell sequencing in microbiome studies – single-cell sequencing along with short-read sequencing to improve strain resolution in complex microbiomes
Current Projects
Harnessing single-cell genomics and shotgun metagenomics to develop an optimised and integrated framework for improved strain-resolved genome recovery from microbiomes (SingleShot)
Education
- Project Management (QQI Level 6) – DCM Learning, Dublin, Ireland 2022
- Doctor of Philosophy (Microbiology) – University of Calcutta 2018
- Master of Science (Microbiology) – University of Calcutta 2011
- Bachelor of Science (Microbiology) – University of Calcutta 2009
Professional Membership
Topic Editor, Frontiers in Nutrition: PIMENTO June 2024
Topic Editor, Frontiers in Microbiology August 2024
Associate Editor, Critical Reviews in Microbiology 2023-Present
INFOGEST 2022-Present
Associate Faculty Member, Faculty Opinions Microbiology, H1 Connect 2021-Present
American Society of Microbiology 2016-2017
Institute of Food Technology 2023-2024
ORCID: https://orcid.org/0000-0002-8996-9971
ResearchGate: https://www.researchgate.net/profile/Arghya-Mukherjee-8
Google Scholar: https://scholar.google.com/citations?user=cPgGeHMAAAAJ&hl=en
- Mukherjee A*, Breselge S*, Dimidi E, Marco ML, Cotter PD. Fermented foods and gastrointestinal health: underlying mechanisms. Nature Reviews Gastroenterology & Hepatology 2024; 21:248-66 [*Equal contribution]
- Mukherjee A, Lordan C, Ross RP, Cotter PD. Gut microbes from the phylogenetically diverse genus Eubacterium and their various contributions to gut health. Gut Microbes 2020; 12:1802866.
- Mukherjee A, Gómez-Sala B, O’Connor EM, Kenny JG, Cotter PD. Global Regulatory Frameworks for Fermented Foods: A Review. Frontiers in nutrition 2022; 9:902642.
- Iyer A*, Mukherjee A*, Gómez-Sala B, O’Connor EM, Kenny JG, Cotter PD. The impact of live dietary microbes on health: A scoping review. J Food Sci 2024; 89:773-92. [*Equal contribution]
- Mukherjee A, Farsi DN, Garcia-Gutierrez E, Akan E, Millan JAS, Angelovski L, et al. Impact of fermented foods consumption on gastrointestinal wellbeing in healthy adults: a systematic review and meta-analysis. Frontiers in nutrition; 12:1668889.
- Leali NF*, Mukherjee A*, Crispie F, Allendez G, Amoruso A, Monzani R, et al. Characterising the functional potential of fermented blueberry juice and its impact on the gut microbiota in an ex vivo colon model. Food Research International 2026; 231:118696. [*Equal contribution]
- Mukherjee A, Leali NF, Salvetti E, Torriani S, Cotter PD, Mathur H. OPTIMATRIX v2.0: Optimised protocol to mitigate microbial blooms in the micro-Matrix bioreactor platform used as an ex vivo human distal colon model. MethodsX 2025; 14:103275.
- D’Ugo E, Mukherjee A, Giuseppetti R, Tucci M, Bucci P, Aulenta F, et al. Integration of satellite surveillance and metagenomics for the monitoring and protection of water basins from oil spills. Environmental Advances 2024:100498.
- Mukherjee A, Chettri B, Langpoklakpam JS, Basak P, Prasad A, Mukherjee AK, et al. Bioinformatic approaches including predictive metagenomic profiling reveal characteristics of bacterial response to petroleum hydrocarbon contamination in diverse environments. Scientific reports 2017; 7:1-22.
- Chakraborty A*, Bera A*, Mukherjee A*, Basak P, Khan I, Mondal A, et al. Changing bacterial profile of Sundarbans, the world heritage mangrove: impact of anthropogenic interventions. World Journal of Microbiology and Biotechnology 2015; 31:593-610. (*equal first authorship)